Birds do it, bees do it, worms and ciliates do it too: DNA methylation from unexpected corners of the tree of life

See related research articles http://genomebiology.com/2012/13/10/R99 webcite and http://genomebiology.com/2012/13/10/R100 webciteDNA methylation refers to a chemical modification of genomic DNA by the addition of a methyl (-CH3) group to specific nucleotide bases. The most common form of DNA methylation is cytosine methylation, occurring predominantly in CpGs in animal genomes, and enriched in CpHs and CpHpHs (where H stands for bases other than G) in plant and fungal genomes [1].DNA methylation is phylogenetically highly variable. Notably, most of the commonly used non-mammalian model organisms (yeast, fruit fly, and worm but not Arabidopsis) lack genomic DNA methylation. Genome projects that have emerged in the past few years, however, have repeatedly demonstrated that DNA methylation is far more widespread than one would expect from the lack of DNA methylation in model organisms. These studies converge to establish DNA methylation as an evolutionarily ancient regulatory mechanism and indicate that the loss of DNA methylation is derived and is generally a lineage-restricted evolutionary event.The distribution of DNA methylation enzymes across the tree of life provides a complementary view. Methylations of DNA templates are achieved by two distinct classes of DNA methylation enzymes, dnmt1 and dnmt3. These enzymes are widely distributed in eukaryotic genomes, yet are frequently gained or lost from genomes as a result of gene duplications and losses in specific lineages [2]. Species exhibiting functional DNA methylation generally encode a 'complete' set of both dnmt1 and dnmt3 in their genomes. Species lacking DNA methylation, such as the model nematode Caenorhabditis elegans, seem to have lost DNA methylation enzymes from their genomes. Furthermore, functional studies have begun to elucidate the regulatory significance of DNA methylation in processes such as alternative splicing, gene expression, and phenotypic plasticity in non-model organisms [3,4].Two articles